Coronary artery disease is a leading global cause of mortality. It can be diagnosed by fractional flow reserve (FFR) estimation using computed tomography (CT) angiography. This systematic review aims to review the literature about the diagnostic efficacy of FFR estimation using CT scan (FFR-CT) for the diagnosis of coronary artery disease. The dual databases of Medline and Cochrane Central Register of Controlled Trials were searched for relevant literature from their inception till August 15, 2017. The methodological quality was assessed using the Cochrane risk of bias tool. Pooled estimates of specificity and sensitivity were assessed with the corresponding 95% confidence intervals (CI). After careful screening, five studies involving a total of 296 patients were included in the study. For FFR-CT, on meta-analysis of the pooled risk ratio per patient, random-effects model value was 3.79 (95% CI, 2.93–4.90) and odds ratio per patient was 11.78 (95% CI, 8.08–17.17). The odds ratio by year to see if heterogeneity is due to sample size was 2.50 (95% CI, 1.06–5.91). FFR-CT appears to be a reliable and efficacious noninvasive imaging modality, as it demonstrates high accuracy in the determination of anatomy and lesion-specific ischemia, which justifies the performance of additional randomized controlled trials to evaluate the clinical benefits of FFR-CT-guided coronary revascularization.